Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 1.7 mM DG3ATG3ACACAG4ACG3, 10 mM potassium phosphate, 40 mM potassium chloride | 90% H2O/10% D2O | 50 | 6.8 | ambient | 298 | |
2 | 2D 1H-1H NOESY | 2.3 mM DG3ATG3ACACAG4ACG3, 10 mM potassium phosphate, 40 mM potassium chloride | 100% D2O | 50 | 6.8 | ambient | 298 | |
3 | 2D DQF-COSY | 2.3 mM DG3ATG3ACACAG4ACG3, 10 mM potassium phosphate, 40 mM potassium chloride | 100% D2O | 50 | 6.8 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | Uniform NMR System | 800 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | VnmrJ |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | processing | VnmrJ | Varian | |
2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | peak picking | Sparky | Goddard | |
5 | structure solution | Amber | 9 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |
6 | refinement | Amber | 9 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |